That happens since Intrigue came out and was reported a lot of times already ...

Its actually been happening since Mercenaries came out. You just did not see it very often due to the AI not actually buying many of the planet buffing mercs, maybe a half hearted fix, AI not buying planet mercs, but who knows. i wont hold my breath on this getting fixed any time soon.

It happens without fail in every game. AI always uses government ships to explore instead of using the boosting capabilities and it (AI) NEVER employs planet boosting mercenaries in their primary role. The Merc colony ships have become an extra resource for the human player, with retribution's lower limit on growth that has become a major plus for the human on games at lower than genius settings.